The role of spatial nuclear organisation in genome function

Lead Research Organisation: University of Edinburgh

Abstract

The linear sequence map of the DNA that makes up our human genome is an incomplete description of our genetic information. This is because information on genome function and gene regulation is also encoded in the way that the DNA sequence is folded up with proteins within chromosomes and within the cell nucleus. Our work tries to understand the three-dimensional folding of the genome, and how this controls how our genome functions in normal development and how this may be perturbed in disease. A particularly important question is how genes are controlled in time and space by elements in our genome called enhancers that can located far away from the genes that they control. This is an important area of human genetics because most of the common genetic variation between individuals in a population that affects our life-time risk of developing disease, lies in enhancers. A prominent feature of our work is the use of visual assays to investigate how the genome is folded up. To do this we combine fluorescence in situ hybridisation (FISH) and digital microscopy with the use of automated image analysis software.

Technical Summary

The regulation of gene expression is controlled by enhancers that are often located at very large genomic distance from their target genes. Mutation of enhancers underlies many cases of severe human developmental disorders and common sequence variation at enhancers contributes to a large proportion of complex genetic disease and quantitative traits. Functional interpretation of the DNA sequence variation revealed by large-scale whole human genome sequencing efforts requires a much better understanding of how enhancers work and is a major challenge in human genomics.
We will probe mechanisms of chromosome folding linked to enhancer function and to spatial positioning in the nucleus. To gain mechanistic insight into the molecular events required to activate a gene from a distance, we will use multi-disciplinary approaches – from high-throughput chromatin profiling to advanced optical imaging - integrated with synthetic biology tools that allow us to dissect cause/consequence relationships between chromatin organisation and genome function. We will test models of enhancer-promoter communication and will determine what factors are required to bind at enhancers in order to instigate the different steps of transcription. We will focus on exemplar loci that are paradigms for long-range cis-regulation (e.g. Shh and Pax6) but, with collaborators, will also help drive the functional follow-up of loci identified by genome-wide association studies (GWAS) and that involve common genetic variation at enhancers.
 
Description Scientific Advisory Board Sanger Institute
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
Description Understanding the role of nuclear pores in 3D genome organisation and function
Amount £509,382 (GBP)
Funding ID 217120/Z/19/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2019 
End 08/2023
 
Title QSTARZ enhancer reporter assay cassette 
Description We developed Q-STARZ (Quantitative Spatial and Temporal Assessment of Regulatory element activity in Zebrafish), a new and significantly improved design of a previous transgenic reporter assay, based upon targeted integration of a dual-CRE dual-reporter cassette into a pre-defined site in the zebrafish genome. A unique feature of this design is the single transgenic cassette containing both wild-type and mutant CREs, separated by strong insulator sequences, with the transcriptional potential of both CREs read out as expression of different fluorescent proteins. Qualitative and quantitative activity of the two CRE alleles is analyzed from eGFP/mCherry fluorescence in real-time by live imaging of embryos obtained from the founder (F0) lines bearing the dual CRE dual-reporter cassette. This allows robust, unbiased assessment of spatial and temporal activities of both CREs using a single transgenic line, thereby reducing animal usage by up to 75% compared to the previous design. We utilize disease-associated mutations in well characterized CREs from the PAX6 and SHH loci to demonstrate the salient features of the Q-STARZ method. 
Type Of Material Technology assay or reagent 
Year Produced 2021 
Provided To Others? Yes  
Impact Too early to tell, but we have already received requests for the constructs for this assay from other researchers. We intend to deposit the relevant constructs in Addgene 
 
Title NPD 
Description Expertly curated database for mammalian nuclear proteins 
Type Of Material Database/Collection of data 
Year Produced 2010 
Provided To Others? Yes  
Impact Not known 
URL http://npd.hgu.mrc.ac.uk/user/about
 
Description CRUK Edinburgh Cancer Research Centre 
Organisation Cancer Research UK
Department Edinburgh Cancer Research UK Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution We provided the research hypothesis, expertise in genome spatial organiosation and the advanced imaging methodology
Collaborator Contribution The collaborators brought the cell system for replicative senescence, the domain-specific expertise and the assays for the senescence-associated secretory phenotype
Impact Publication:
Start Year 2018
 
Description Synthetic variation at the PAX6 locus 
Organisation NYU Langone Medical Center
Country United States 
Sector Academic/University 
PI Contribution Functional testing of engineered PAX6 loci in vertebrate cell and organism systems
Collaborator Contribution Joint NSF/BBSRC grant. NYU collaborator is providing the expertise in synthetic biology using S.cerevisiae
Impact Too early for outputs
Start Year 2020
 
Title Coolpup.py 
Description Algorithm for efficient pile-up of Hi-C data 
Type Of Technology Webtool/Application 
Year Produced 2020 
Open Source License? Yes  
Impact Widely used and being cited in publications 
 
Description Discovery Zone, Chelsea Flower Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Exhibit at the Chelsea flower show to celebrate the centenary of the Genetics Society. The genetics of flower colour and form
Year(s) Of Engagement Activity 2019
URL https://www.ed.ac.uk/mrc-human-genetics-unit/news-and-events/latest-news/genetics-garden-wins-silver...
 
Description MRC Festival of Science 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Patients, carers and/or patient groups
Results and Impact "Shining a light on Genetic Disorders". Dialogue between researchers and patients.
Year(s) Of Engagement Activity 2019
URL https://www.ed.ac.uk/mrc-human-genetics-unit/news-and-events/latest-news/shining-a-light-on-genetics...
 
Description Podcast 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Podcast for the Lonely Pipettes - about career path and research culture
Year(s) Of Engagement Activity 2021
URL https://podcasts.apple.com/gb/podcast/tlp-7-its-okay-to-be-wrong-wendy-bickmore/id1532120809?i=10005...
 
Description Press release and press coverage 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Press release on our work on senescence was widely picked up by the national and international press.

https://www.edinburghnews.scotsman.com/news/health/edinburgh-university-study-sheds-light-on-how-to-stop-damaging-effects-of-ageing-1-4873531 (includes a quote from CRUK)
https://www.irishexaminer.com/breakingnews/world/damaging-effects-of-ageing-could-be-prevented-scientists-claim-904424.html
https://www.independent.ie/life/health-wellbeing/damaging-effects-of-ageing-could-be-prevented-new-research-37816323.html
https://nypost.com/2019/02/14/miracle-anti-aging-pill-nearer-reality-after-breakthrough/
https://www.breakingnews.ie/world/damaging-effects-of-ageing-could-be-prevented-scientists-claim-904424.html
https://www.news-medical.net/news/20190215/Cell-manipulation-could-soon-halt-or-reverse-aging.aspx
https://www.sciencedaily.com/releases/2019/02/190214100036.htm
Year(s) Of Engagement Activity 2019
 
Description Public talk on the future of Human Genetics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Field, farm and family debate associated with the 100 years of Genetics conference.
Year(s) Of Engagement Activity 2019
 
Description Radio interview 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview about our work on senescence on Radio 4's Today programme.
Year(s) Of Engagement Activity 2019
 
Description Radio interview (BBC Scotland) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Radio interview on Good Morning Scotland (BBC Scotland) about our work on senescence
Year(s) Of Engagement Activity 2019
 
Description Radio interview (World Service) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Radio interview on the World Service about our work on senescence
Year(s) Of Engagement Activity 2019
 
Description Visit from Scottish Government Cabinet Secretary flor Health 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Visit to the Genomic Data Analysis Centre providing genome interpretation for rare disease for NHS Scotland.
Year(s) Of Engagement Activity 2019
URL https://www.ed.ac.uk/mrc-human-genetics-unit/news-and-events/latest-news/jeane-freeman-msp-mrc-visit